iRefIndex Release Process

From irefindex

The release process consists of a number of activities.

Building the Database

See iRefIndex Build Process for details.

Generating Output Files and Statistics

See iRefIndex Output and Statistics for details.

Testing the Output

  • Checking for errors and log messages
  • Web services
  • Spot checks
  • Counting XML tags
  • Validation

PSI-MI MITAB files are validated using scripts available at [1]

PSI-MI XML files are validated using the validator at [2]

Posting the Output Files

The output files themselves are made available on the iRefIndex FTP site as described on the iRefIndex information page. This involves making a directory in the following local location:


For example, for the iRefIndex 3.0 release, the following directory hierarchy is created:

mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab

The data files are then copied into this new directory. For example:

cp /home/irefindex/output/*.zip /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab/

A README file should be placed in the directory containing a link to the format description. For example:

Please see

The symbolic link indicating the location of the current release needs to be updated. For iRefIndex 3.0 this is done as follows:

cd /biotek/proteas/ftp/irefindex/data
rm current
ln -s archive/release_3.0 current

Finally, the release file must be updated to indicate the current release number. For iRefIndex 3.0 this contains the following text:


Optional/Experimental Output Files

Additional PSI-MI-XML files may be made available within the release directory within a subdirectory created as follows (for iRefIndex 3.0):

mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi25xml

(Instructions on copying these files will be added in future.)

A README file should be placed in the directory with the following form:

Please see

(This directory contains a sample of iRefIndex data in PSI-MI 2.5 XML format for testing purposes only)

Updating the Wiki

The iRefIndex page will need updating with version-specific references such as the following:

  • README_iRefIndex_MITAB_x.y
  • Sources_iRefIndex_x.y
  • README_iRefIndex_Feedback_x.y
  • Statistics_iRefIndex_x.y

New documents will need creating for some of these references.

For new data sources, the text will need editing and a citation reference should be added for the new source.